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SOSUS development was started in 1949 when the US Navy formed the Committee for Undersea Warfare to research anti-submarine warfare. The panel allocated $10 million annually to develop systems to counter the Soviet submarine threat consisting primarily of a large fleet of diesel submarines. They decided on a system to monitor low-frequency sound in the SOFAR channel using multiple listening sites equipped with hydrophones and a processing facility that could detect submarine positions by triangulation[dubious– discuss] over hundreds of miles.

At MIT in 1950, the committee sponsored Project Hartwell, named for the Hartwell Farms restaurant in Lexington, MA, where some of the initial steps were planned.[1] In November, they selected Western Electric to build a demonstration system, and the first six element hydrophone array was installed on the island of Eleuthera in the Bahamas. Meanwhile, Project Jezebel at Bell Labs and Project Michael at Columbia University focused on studying long range acoustics in the ocean.

By 1952, enough progress resulted in top secret plans to deploy six arrays in the North Atlantic basin, and the classified name SOSUS was used. The number of arrays was increased to nine later in the year, and Royal Navy and USN ships, including USS Neptune and USS Peregrine, started laying the cabling under the cover of Project Caesar. In 1953, Jezebel's research had developed an additional high-frequency system for direct plotting of ships passing over the stations, intended to be installed in narrows and straits, called Project Colossus.

SOSUS systems consisted of bottom mounted hydrophone arrays connected by underwater cables to facilities ashore. The individual arrays were installed primarily on continental slopes and seamounts at locations optimized for undistorted long range acoustic propagation. The combination of location within the ocean and the sensitivity of arrays allowed the system to detect acoustic power of less than a watt at ranges of several hundred kilometres (The system is so sensitive that it can even detect the presence of Soviet/Russian Tu-95 Bear 4-engine bombers flying overhead; the tips of the bombers's long propellers exceed the speed of sound, creating sonic booms as they rotate. These sonic booms reach the surface of the ocean below, which then transmits the sonic shocks to the underwater hydrophones.[2]).

In 1985, the Fixed Distributed System (FDS) test array became operational and the first SURTASS patrol began. The name for the overall system had become Integrated Undersea Surveillance System (IUSS).

Given its criticality to Cold War operations against the Soviet Navy's submarine fleet, SOSUS / IUSS remained highly classified from its inception and the purpose and activities of the various NAVFACs was not publicly acknowledged nor commonly known outside of the U.S. Navy's submarine fleet, its cruiser/destroyer/frigate fleet, and its antisubmarine warfare aircraft forces until the end of the Cold War. In 1991, the system mission was declassified and the next year it began reporting whale detections and SOSUS work stations began replacing paper lofargrams. The Advanced Deployable System became operational as part of IUSS in 1996.

SOSUS was gradually condensed into a smaller number of monitoring stations during the 1970s and 1980s. However, the SOSUS arrays themselves were based upon technology that could only be upgraded irregularly. With the ending of the Cold War in the 1990s, the immediate need for SOSUS decreased, and the focus of the US Navy also turned toward a system that was deployable on a theatre basis. In effect, the end of the Cold War eliminated much of the justification for maintaining IUSS at its full capability, with the existence and capabilities of SOSUS and IUSS being declassified in 1991.[3] Although officially declassified in 1991, by that time IUSS and SOSUS had long been an open secret.[3]

Commander, Undersea Surveillance (CUS), operates as the immediate superior in command (ISIC) for all IUSS sites, whereas operational command of those same sites is held by Commander, Submarine Force, U.S. Pacific Fleet (COMSUBPAC).